Hi, I just recently beat X and I went to the Pokemon Village to go and find Mewtwo so that I could capture it. I found it and started battling, once it was to about half of its HP, I used an ultra ball but it failed and then I used my surviving Aeigislash's Shadow Sneak and it turned into a critical hit and it made Mewtwo faint...I don't know how to get it back...I could have used my save file but I don't know where I last saved... PLEASE HELP!

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No you still have a chance to get it. Beating the Elite 4 again will bring back any legendary that you accidentally fainted. Beat the Pokemon League again and Mewtwo should come back. Save infront of him this time.